Survival microbiome data from 150 individuals with longitudinal measurements

Source: R/miaTime.R

Simulated dataset based on a Crohn's disease microbiome study. The dataset is right-censored and includes time-to-event data, representing either the occurrence of disease or censoring. It contains 150 individuals and 48 taxa. The dataset originates from the coda4microbiome package under the name "data_survival".

data(crohn_survival)

Format

The dataset is in the TreeSummarizedExperiment format.

Value

Loads the dataset in R.

Details

Sample metadata includes the following information:

  • diagnosis: Indicates whether an individual has Crohn’s disease (CD) or is a control.

  • event: Binary variable indicating disease status (1 = Crohn’s Disease, 0 = Control).

  • event_time: The time of event occurrence or censoring (unitless time).

Taxa data do not include additional taxonomy information.

References

Calle ML et al. (2023) coda4microbiome: compositional data analysis for microbiome cross-sectional and longitudinal studies. BMC Bioinformatics, 24(82). https://doi.org/10.1186/s12859-023-05205-3

Gevers D et al. (2018) The Treatment-Naive Microbiome in New-Onset Crohn’s Disease. Cell Host & Microbe, 15(4). #' https://doi.org/10.1016/j.chom.2014.02.005